import json
import logging
import mimetypes
import os
import shutil
import string
import tempfile
from inspect import isclass
from typing import (
Any,
Callable,
Dict,
Generator,
IO,
Iterable,
List,
Optional,
Tuple,
TYPE_CHECKING,
Union,
)
from markupsafe import escape
from typing_extensions import Literal
from galaxy import util
from galaxy.datatypes.metadata import (
MetadataElement, # import directly to maintain ease of use in Datatype class definitions
)
from galaxy.datatypes.protocols import (
DatasetHasHidProtocol,
DatasetProtocol,
HasClearAssociatedFiles,
HasCreatingJob,
HasExt,
HasExtraFilesAndMetadata,
HasFileName,
HasInfo,
HasMetadata,
HasName,
)
from galaxy.datatypes.sniff import (
build_sniff_from_prefix,
FilePrefix,
)
from galaxy.exceptions import ObjectNotFound
from galaxy.util import (
compression_utils,
file_reader,
FILENAME_VALID_CHARS,
inflector,
iter_start_of_line,
to_content_disposition,
unicodify,
UNKNOWN,
)
from galaxy.util.bunch import Bunch
from galaxy.util.compression_utils import FileObjType
from galaxy.util.markdown import (
indicate_data_truncated,
literal_via_fence,
)
from galaxy.util.zipstream import ZipstreamWrapper
from . import (
dataproviders as p_dataproviders,
metadata,
)
if TYPE_CHECKING:
from galaxy.datatypes.display_applications.application import DisplayApplication
from galaxy.datatypes.registry import Registry
XSS_VULNERABLE_MIME_TYPES = [
"image/svg+xml", # Unfiltered by Galaxy and may contain JS that would be executed by some browsers.
"application/xml", # Some browsers will evaluate SVG embedded JS in such XML documents.
]
DEFAULT_MIME_TYPE = "text/plain" # Vulnerable mime types will be replaced with this.
log = logging.getLogger(__name__)
# Valid first column and strand column values vor bed, other formats
col1_startswith = ["chr", "chl", "groupun", "reftig_", "scaffold", "super_", "vcho"]
valid_strand = ["+", "-", "."]
DOWNLOAD_FILENAME_PATTERN_DATASET = "Galaxy${hid}-[${name}].${ext}"
DOWNLOAD_FILENAME_PATTERN_COLLECTION_ELEMENT = "Galaxy${hdca_hid}-[${hdca_name}__${element_identifier}].${ext}"
DEFAULT_MAX_PEEK_SIZE = 1000000 # 1 MB
Headers = Dict[str, Any]
[docs]
class DatatypeConverterNotFoundException(Exception):
pass
[docs]
class DatatypeValidation:
[docs]
def __init__(self, state: str, message: str) -> None:
self.state = state
self.message = message
[docs]
@staticmethod
def validated() -> "DatatypeValidation":
return DatatypeValidation("ok", "Dataset validated by datatype validator.")
[docs]
@staticmethod
def invalid(message: str) -> "DatatypeValidation":
return DatatypeValidation("invalid", message)
[docs]
@staticmethod
def unvalidated() -> "DatatypeValidation":
return DatatypeValidation(UNKNOWN, "Dataset validation unimplemented for this datatype.")
def __repr__(self) -> str:
return f"DatatypeValidation[state={self.state},message={self.message}]"
[docs]
def validate(dataset_instance: DatasetProtocol) -> DatatypeValidation:
try:
datatype_validation = dataset_instance.datatype.validate(dataset_instance)
except Exception as e:
datatype_validation = DatatypeValidation.invalid(f"Problem running datatype validation method [{str(e)}]")
return datatype_validation
def _is_binary_file(data):
from galaxy.datatypes import binary
return isinstance(data.datatype, binary.Binary) or type(data.datatype) is Data
def _get_max_peek_size(data):
from galaxy.datatypes import (
binary,
text,
)
max_peek_size = DEFAULT_MAX_PEEK_SIZE # 1 MB
if isinstance(data.datatype, text.Html):
max_peek_size = 50000000 # 50 MB for html
elif isinstance(data.datatype, binary.Binary):
max_peek_size = 100000 # 100 KB for binary
return max_peek_size
def _get_file_size(data):
file_size = int(data.dataset.file_size or 0)
if file_size == 0:
if data.dataset.object_store:
file_size = data.dataset.object_store.size(data.dataset)
else:
file_size = os.stat(data.get_file_name()).st_size
return file_size
[docs]
@p_dataproviders.decorators.has_dataproviders
class Data(metaclass=DataMeta):
"""
Base class for all datatypes. Implements basic interfaces as well
as class methods for metadata.
>>> class DataTest( Data ):
... MetadataElement( name="test" )
...
>>> DataTest.metadata_spec.test.name
'test'
>>> DataTest.metadata_spec.test.desc
'test'
>>> type( DataTest.metadata_spec.test.param )
<class 'galaxy.model.metadata.MetadataParameter'>
"""
edam_data = "data_0006"
edam_format = "format_1915"
file_ext = "data"
is_subclass = False
# Data is not chunkable by default.
CHUNKABLE = False
#: Dictionary of metadata fields for this datatype
metadata_spec: metadata.MetadataSpecCollection
# Add metadata elements
MetadataElement(
name="dbkey",
desc="Database/Build",
default="?",
param=metadata.DBKeyParameter,
multiple=False,
optional=True,
no_value="?",
)
# Stores the set of display applications, and viewing methods, supported by this datatype
supported_display_apps: Dict[str, Any] = {}
# The dataset contains binary data --> do not space_to_tab or convert newlines, etc.
# Allow binary file uploads of this type when True.
is_binary: Union[bool, Literal["maybe"]] = True
# Composite datatypes
composite_type: Optional[str] = None
composite_files: Dict[str, Any] = {}
primary_file_name = "index"
# Allow user to change between this datatype and others. If left to None,
# datatype change is allowed if the datatype is not composite.
allow_datatype_change: Optional[bool] = None
# A per datatype setting (inherited): max file size (in bytes) for setting optional metadata
_max_optional_metadata_filesize = None
# Display behavior when preview=True: "inline" (can be displayed in browser),
# "download" (always triggers download), or None (default behavior)
display_behavior: Optional[Literal["inline", "download"]] = None
# Trackster track type.
track_type: Optional[str] = None
# Data sources.
data_sources: Dict[str, str] = {}
dataproviders: Dict[str, Any]
[docs]
def __init__(self, **kwd):
"""Initialize the datatype"""
self.supported_display_apps = self.supported_display_apps.copy()
self.composite_files = self.composite_files.copy()
self.display_applications = {}
[docs]
@classmethod
def is_datatype_change_allowed(cls) -> bool:
"""
Returns the value of the `allow_datatype_change` class attribute if set
in a subclass, or True iff the datatype is not composite.
"""
if cls.allow_datatype_change is not None:
return cls.allow_datatype_change
return cls.composite_type is None
[docs]
@classmethod
def get_display_behavior(cls) -> str:
"""
Returns the display behavior for this datatype.
If display_behavior is set on the class, returns that value.
Otherwise, returns "inline" for text-based types and "download" for binary types.
"""
if cls.display_behavior is not None:
return cls.display_behavior
# Default behavior based on whether the datatype is binary
if cls.is_binary is True:
return "download"
else:
return "inline"
[docs]
def dataset_content_needs_grooming(self, file_name: str) -> bool:
"""This function is called on an output dataset file after the content is initially generated."""
return False
[docs]
def groom_dataset_content(self, file_name: str) -> None:
"""This function is called on an output dataset file if dataset_content_needs_grooming returns True."""
max_optional_metadata_filesize = property(get_max_optional_metadata_filesize, set_max_optional_metadata_filesize)
[docs]
def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
"""
Set the peek and blurb text
"""
if not dataset.dataset.purged:
dataset.peek = ""
dataset.blurb = "data"
else:
dataset.peek = "file does not exist"
dataset.blurb = "file purged from disk"
[docs]
def display_peek(self, dataset: DatasetProtocol) -> str:
"""Create HTML table, used for displaying peek"""
if not dataset.peek:
return "Peek not available"
out = ['<table cellspacing="0" cellpadding="3">']
try:
data = dataset.peek
lines = data.splitlines()
for line in lines:
line = line.strip()
if not line:
continue
out.append(f"<tr><td>{escape(unicodify(line, 'utf-8'))}</td></tr>")
out.append("</table>")
return "".join(out)
except Exception as exc:
return f"Can't create peek: {unicodify(exc)}"
def _archive_main_file(
self, archive: ZipstreamWrapper, display_name: str, data_filename: str
) -> Tuple[bool, str, str]:
"""Called from _archive_composite_dataset to add central file to archive.
Unless subclassed, this will add the main dataset file (argument data_filename)
to the archive, as an HTML file with its filename derived from the dataset name
(argument outfname).
Returns a tuple of boolean, string, string: (error, msg, messagetype)
"""
error, msg, messagetype = False, "", ""
archname = f"{display_name}.html" # fake the real nature of the html file
try:
archive.write(data_filename, archname)
except OSError:
error = True
log.exception("Unable to add composite parent %s to temporary library download archive", data_filename)
msg = "Unable to create archive for download, please report this error"
messagetype = "error"
return error, msg, messagetype
def _archive_composite_dataset(
self, trans, data: DatasetHasHidProtocol, headers: Headers, do_action: str = "zip"
) -> Tuple[Union[ZipstreamWrapper, str], Headers]:
# save a composite object into a compressed archive for downloading
outfname = data.name[0:150]
outfname = "".join(c in FILENAME_VALID_CHARS and c or "_" for c in outfname)
archive = ZipstreamWrapper(
archive_name=outfname,
upstream_mod_zip=trans.app.config.upstream_mod_zip,
upstream_gzip=trans.app.config.upstream_gzip,
)
error = False
msg = ""
ext = data.extension
path = data.get_file_name()
efp = data.extra_files_path
# Add any central file to the archive,
display_name = os.path.splitext(outfname)[0]
if not display_name.endswith(ext):
display_name = f"{display_name}_{ext}"
error, msg = self._archive_main_file(archive, display_name, path)[:2]
if not error:
# Add any child files to the archive,
for fpath, rpath in self.__archive_extra_files_path(extra_files_path=efp):
try:
archive.write(fpath, rpath)
except OSError:
error = True
log.exception("Unable to add %s to temporary library download archive", rpath)
msg = "Unable to create archive for download, please report this error"
continue
if not error:
headers.update(archive.get_headers())
return archive, headers
return trans.show_error_message(msg), headers
def __archive_extra_files_path(self, extra_files_path: str) -> Generator[Tuple[str, str], None, None]:
"""Yield filepaths and relative filepaths for files in extra_files_path"""
for root, _, files in os.walk(extra_files_path):
for fname in files:
fpath = os.path.join(root, fname)
rpath = os.path.relpath(fpath, extra_files_path)
yield fpath, rpath
def _serve_raw(
self, dataset: DatasetHasHidProtocol, to_ext: Optional[str], headers: Headers, **kwd
) -> Tuple[IO, Headers]:
headers["Content-Length"] = str(os.stat(dataset.get_file_name()).st_size)
headers["content-type"] = (
"application/octet-stream" # force octet-stream so Safari doesn't append mime extensions to filename
)
filename = self._download_filename(
dataset,
to_ext,
hdca=kwd.get("hdca"),
element_identifier=kwd.get("element_identifier"),
filename_pattern=kwd.get("filename_pattern"),
)
headers["Content-Disposition"] = to_content_disposition(filename)
return open(dataset.get_file_name(), mode="rb"), headers
[docs]
def to_archive(self, dataset: DatasetProtocol, name: str = "") -> Iterable:
"""
Collect archive paths and file handles that need to be exported when archiving `dataset`.
:param dataset: HistoryDatasetAssociation
:param name: archive name, in collection context corresponds to collection name(s) and element_identifier,
joined by '/', e.g 'fastq_collection/sample1/forward'
"""
rel_paths = []
file_paths = []
if dataset.datatype.composite_type or dataset.extension.endswith("html"):
main_file = f"{name}.html"
rel_paths.append(main_file)
file_paths.append(dataset.get_file_name())
for fpath, rpath in self.__archive_extra_files_path(dataset.extra_files_path):
rel_paths.append(os.path.join(name, rpath))
file_paths.append(fpath)
else:
rel_paths.append(f"{name or dataset.get_file_name()}.{dataset.extension}")
file_paths.append(dataset.get_file_name())
return zip(file_paths, rel_paths)
def _serve_file_download(self, headers, data, trans, to_ext, file_size, **kwd):
composite_extensions = trans.app.datatypes_registry.get_composite_extensions()
composite_extensions.append("html") # for archiving composite datatypes
composite_extensions.append("tool_markdown") # basically should act as an HTML datatype in this capacity
composite_extensions.append("data_manager_json") # for downloading bundles if bundled.
composite_extensions.append("directory") # for downloading directories.
composite_extensions.append("zarr") # for downloading zarr directories.
if data.extension in composite_extensions:
return self._archive_composite_dataset(trans, data, headers, do_action=kwd.get("do_action", "zip"))
else:
headers["Content-Length"] = str(file_size)
filename = self._download_filename(
data,
to_ext,
hdca=kwd.get("hdca"),
element_identifier=kwd.get("element_identifier"),
filename_pattern=kwd.get("filename_pattern"),
)
headers["content-type"] = (
"application/octet-stream" # force octet-stream so Safari doesn't append mime extensions to filename
)
headers["Content-Disposition"] = to_content_disposition(filename)
return open(data.get_file_name(), "rb"), headers
def _serve_binary_file_contents_as_text(self, trans, data, headers, file_size, max_peek_size):
headers["content-type"] = "text/html"
with open(data.get_file_name(), "rb") as fh:
return (
trans.fill_template_mako(
"/dataset/binary_file.mako",
data=data,
file_contents=fh.read(max_peek_size),
file_size=util.nice_size(file_size),
truncated=file_size > max_peek_size,
),
headers,
)
def _serve_file_contents(self, trans, data, headers, preview, file_size, max_peek_size):
from galaxy.datatypes import images
preview = util.string_as_bool(preview)
if not preview or isinstance(data.datatype, images.Image) or file_size < max_peek_size:
return self._yield_user_file_content(trans, data, data.get_file_name(), headers), headers
with compression_utils.get_fileobj(data.get_file_name(), "rb") as fh:
# preview large text file
headers["content-type"] = "text/html"
return (
trans.fill_template_mako(
"/dataset/large_file.mako",
truncated_data=fh.read(max_peek_size),
data=data,
),
headers,
)
[docs]
def display_data(
self,
trans,
dataset: DatasetHasHidProtocol,
preview: bool = False,
filename: Optional[str] = None,
to_ext: Optional[str] = None,
**kwd,
):
"""
Displays data in central pane if preview is `True`, else handles download.
Datatypes should be very careful if overriding this method and this interface
between datatypes and Galaxy will likely change.
TODO: Document alternatives to overriding this method (data
providers?).
"""
headers = kwd.get("headers", {})
# Prevent IE8 from sniffing content type since we're explicit about it. This prevents intentionally text/plain
# content from being rendered in the browser
headers["X-Content-Type-Options"] = "nosniff"
if filename and filename != "index":
# For files in extra_files_path
extra_dir = dataset.dataset.extra_files_path_name
file_path = trans.app.object_store.get_filename(dataset.dataset, extra_dir=extra_dir, alt_name=filename)
if os.path.exists(file_path):
if os.path.isdir(file_path):
with tempfile.NamedTemporaryFile(
mode="w", delete=False, dir=trans.app.config.new_file_path, prefix="gx_html_autocreate_"
) as tmp_fh:
tmp_file_name = tmp_fh.name
dir_items = sorted(os.listdir(file_path))
base_path, item_name = os.path.split(file_path)
tmp_fh.write(
f"<html><head><h3>Directory {escape(item_name)} contents: {len(dir_items)} items</h3></head>\n"
)
tmp_fh.write('<body><p/><table cellpadding="2">\n')
for index, fname in enumerate(dir_items):
if index % 2 == 0:
bgcolor = "#D8D8D8"
else:
bgcolor = "#FFFFFF"
# Can't have an href link here because there is no route
# defined for files contained within multiple subdirectory
# levels of the primary dataset. Something like this is
# close, but not quite correct:
# href = url_for(controller='dataset', action='display',
# dataset_id=trans.security.encode_id(dataset.dataset.id),
# preview=preview, filename=fname, to_ext=to_ext)
tmp_fh.write(f'<tr bgcolor="{bgcolor}"><td>{escape(fname)}</td></tr>\n')
tmp_fh.write("</table></body></html>\n")
return self._yield_user_file_content(trans, dataset, tmp_file_name, headers), headers
mime = mimetypes.guess_type(file_path)[0]
if not mime:
try:
mime = trans.app.datatypes_registry.get_mimetype_by_extension(file_path.split(".")[-1])
except Exception:
mime = "text/plain"
self._clean_and_set_mime_type(trans, mime, headers) # type: ignore[arg-type]
return self._yield_user_file_content(trans, dataset, file_path, headers), headers
else:
raise ObjectNotFound(f"Could not find '{filename}' on the extra files path {file_path}.")
self._clean_and_set_mime_type(trans, dataset.get_mime(), headers)
downloading = to_ext is not None
file_size = _get_file_size(dataset)
if not os.path.exists(dataset.get_file_name()):
raise ObjectNotFound(f"File Not Found ({dataset.get_file_name()}).")
if downloading:
trans.log_event(f"Download dataset id: {str(dataset.id)}")
return self._serve_file_download(headers, dataset, trans, to_ext, file_size, **kwd)
else: # displaying
trans.log_event(f"Display dataset id: {str(dataset.id)}")
max_peek_size = _get_max_peek_size(dataset)
if (
_is_binary_file(dataset) and preview and hasattr(trans, "fill_template_mako")
): # preview file which format is unknown (to Galaxy), we still try to display this as text
return self._serve_binary_file_contents_as_text(trans, dataset, headers, file_size, max_peek_size)
else: # text/html, or image, or display was called without preview flag
return self._serve_file_contents(trans, dataset, headers, preview, file_size, max_peek_size)
[docs]
def display_as_markdown(self, dataset_instance: DatasetProtocol) -> str:
"""Prepare for embedding dataset into a basic Markdown document.
This is a somewhat experimental interface and should not be implemented
on datatypes not tightly tied to a Galaxy version (e.g. datatypes in the
Tool Shed).
Speaking very loosely - the datatype should load a bounded amount
of data from the supplied dataset instance and prepare for embedding it
into Markdown. This should be relatively vanilla Markdown - the result of
this is bleached and it should not contain nested Galaxy Markdown
directives.
If the data cannot reasonably be displayed, just indicate this and do
not throw an exception.
"""
if self.file_ext in {"png", "jpg"}:
return self.handle_dataset_as_image(dataset_instance)
if self.is_binary:
result = "*cannot display binary content*\n"
else:
with open(dataset_instance.get_file_name()) as f:
contents = f.read(DEFAULT_MAX_PEEK_SIZE)
result = literal_via_fence(contents)
if len(contents) == DEFAULT_MAX_PEEK_SIZE:
result += indicate_data_truncated()
return result
def _yield_user_file_content(self, trans, from_dataset: HasCreatingJob, filename: str, headers: Headers) -> IO:
"""This method sets the content type header to text/plain if we don't trust html content."""
if trans.app.config.sanitize_all_html and headers.get("content-type", None) == "text/html":
# Check to see if this dataset's parent job is allowlisted
# We cannot currently trust imported datasets for rendering.
content_type = "text/html"
if from_dataset.creating_job.imported:
content_type = "text/plain"
headers["x-sanitized-job-imported"] = "true"
if not from_dataset.creating_job.tool_id.startswith(tuple(trans.app.config.sanitize_allowlist)):
content_type = "text/plain"
headers["x-sanitized-tool-id"] = from_dataset.creating_job.tool_id
headers["content-type"] = content_type
return open(filename, mode="rb")
def _download_filename(
self,
dataset: DatasetHasHidProtocol,
to_ext: Optional[str] = None,
hdca: Optional[DatasetHasHidProtocol] = None,
element_identifier: Optional[str] = None,
filename_pattern: Optional[str] = None,
) -> str:
if not to_ext or to_ext == "data":
# If a client requests to_ext with the extension 'data', they are
# deferring to the server, set it based on datatype.
to_ext = dataset.extension
template_values = {
"name": dataset.name,
"ext": to_ext,
"hid": dataset.hid,
}
if not filename_pattern:
if hdca is None:
filename_pattern = DOWNLOAD_FILENAME_PATTERN_DATASET
else:
filename_pattern = DOWNLOAD_FILENAME_PATTERN_COLLECTION_ELEMENT
if hdca is not None:
# Use collection context to build up filename.
if element_identifier is not None:
template_values["element_identifier"] = element_identifier
template_values["hdca_name"] = hdca.name
template_values["hdca_hid"] = hdca.hid
return string.Template(filename_pattern).substitute(**template_values)
[docs]
def display_name(self, dataset: HasName) -> str:
"""Returns formatted html of dataset name"""
try:
return escape(unicodify(dataset.name, "utf-8"))
except Exception:
return "name unavailable"
[docs]
def display_info(self, dataset: HasInfo) -> str:
"""Returns formatted html of dataset info"""
try:
# Change new line chars to html
info: str = escape(dataset.info)
if info.find("\r\n") >= 0:
info = info.replace("\r\n", "<br/>")
if info.find("\r") >= 0:
info = info.replace("\r", "<br/>")
if info.find("\n") >= 0:
info = info.replace("\n", "<br/>")
info = unicodify(info, "utf-8")
return info
except Exception:
return "info unavailable"
[docs]
def get_mime(self) -> str:
"""Returns the mime type of the datatype"""
return "application/octet-stream"
[docs]
def add_display_app(self, app_id: str, label: str, file_function: str, links_function: str) -> None:
"""
Adds a display app to the datatype.
app_id is a unique id
label is the primary display label, e.g., display at 'UCSC'
file_function is a string containing the name of the function that returns a properly formatted display
links_function is a string containing the name of the function that returns a list of (link_name,link)
"""
self.supported_display_apps = self.supported_display_apps.copy()
self.supported_display_apps[app_id] = {
"label": label,
"file_function": file_function,
"links_function": links_function,
}
[docs]
def remove_display_app(self, app_id: str) -> None:
"""Removes a display app from the datatype"""
self.supported_display_apps = self.supported_display_apps.copy()
try:
del self.supported_display_apps[app_id]
except Exception:
log.exception(
"Tried to remove display app %s from datatype %s, but this display app is not declared.",
type,
self.__class__.__name__,
)
[docs]
def clear_display_apps(self) -> None:
self.supported_display_apps = {}
[docs]
def add_display_application(self, display_application: "DisplayApplication") -> None:
"""New style display applications"""
assert display_application.id not in self.display_applications, "Attempted to add a display application twice"
self.display_applications[display_application.id] = display_application
[docs]
def get_display_application(self, key: str, default: Optional["DisplayApplication"] = None) -> "DisplayApplication":
return self.display_applications.get(key, default)
[docs]
def get_display_applications_by_dataset(self, dataset: DatasetProtocol, trans) -> Dict[str, "DisplayApplication"]:
rval = {}
for key, value in self.display_applications.items():
value = value.filter_by_dataset(dataset, trans)
if value.links:
rval[key] = value
return rval
[docs]
def get_display_types(self) -> List[str]:
"""Returns display types available"""
return list(self.supported_display_apps.keys())
[docs]
def get_display_label(self, type: str) -> str:
"""Returns primary label for display app"""
try:
return self.supported_display_apps[type]["label"]
except Exception:
return UNKNOWN
[docs]
def as_display_type(self, dataset: DatasetProtocol, type: str, **kwd) -> Union[FileObjType, str]:
"""Returns modified file contents for a particular display type"""
try:
if type in self.get_display_types():
return getattr(self, self.supported_display_apps[type]["file_function"])(dataset, **kwd)
except Exception:
log.exception(
"Function %s is referred to in datatype %s for displaying as type %s, but is not accessible",
self.supported_display_apps[type]["file_function"],
self.__class__.__name__,
type,
)
return f"This display type ({type}) is not implemented for this datatype ({dataset.ext})."
[docs]
def get_display_links(
self, dataset: DatasetProtocol, type: str, app, base_url: str, target_frame: str = "_blank", **kwd
):
"""
Returns a list of tuples of (name, link) for a particular display type. No check on
'access' permissions is done here - if you can view the dataset, you can also save it
or send it to a destination outside of Galaxy, so Galaxy security restrictions do not
apply anyway.
"""
try:
if app.config.enable_old_display_applications and type in self.get_display_types():
return target_frame, getattr(self, self.supported_display_apps[type]["links_function"])(
dataset, type, app, base_url, **kwd
)
except Exception:
log.exception(
"Function %s is referred to in datatype %s for generating links for type %s, but is not accessible",
self.supported_display_apps[type]["links_function"],
self.__class__.__name__,
type,
)
return target_frame, []
[docs]
def get_converter_types(self, original_dataset: HasExt, datatypes_registry: "Registry") -> Dict[str, Dict]:
"""Returns available converters by type for this dataset"""
return datatypes_registry.get_converters_by_datatype(original_dataset.ext)
[docs]
def find_conversion_destination(
self, dataset: DatasetProtocol, accepted_formats: List[str], datatypes_registry, **kwd
) -> Tuple[bool, Optional[str], Any]:
"""Returns ( direct_match, converted_ext, existing converted dataset )"""
return datatypes_registry.find_conversion_destination_for_dataset_by_extensions(
dataset, accepted_formats, **kwd
)
[docs]
def convert_dataset(
self,
trans,
original_dataset: DatasetHasHidProtocol,
target_type: str,
return_output: bool = False,
visible: bool = True,
deps: Optional[Dict] = None,
target_context: Optional[Dict] = None,
history=None,
use_cached_job: bool = False,
):
"""This function adds a job to the queue to convert a dataset to another type. Returns a message about success/failure."""
converter = trans.app.datatypes_registry.get_converter_by_target_type(original_dataset.ext, target_type)
if converter is None:
raise DatatypeConverterNotFoundException(
f"A converter does not exist for {original_dataset.ext} to {target_type}."
)
params, input_name = get_params_and_input_name(converter, deps, target_context)
params[input_name] = original_dataset
# Make the target datatype available to the converter
params["__target_datatype__"] = target_type
# Run converter, job is dispatched through Queue
# Always use cached job if it exists
completed_jobs = converter.completed_jobs(trans, all_params=[params], use_cached_job=use_cached_job)
completed_job = completed_jobs[0] if completed_jobs else None
job, converted_datasets, *_ = converter.execute(
trans,
incoming=params,
set_output_hid=visible,
history=history,
flush_job=False,
completed_job=completed_job,
)
# We should only have a single converted output, but let's be defensive here
n_converted_datasets = len(converted_datasets)
for converted_dataset in converted_datasets.values():
if converted_dataset.extension == "auto" and n_converted_datasets == 1:
converted_dataset.extension = target_type
original_dataset.attach_implicitly_converted_dataset(trans.sa_session, converted_dataset, target_type)
trans.app.job_manager.enqueue(job, tool=converter)
if len(params) > 0:
trans.log_event(f"Converter params: {str(params)}", tool_id=converter.id)
if not visible:
for value in converted_datasets.values():
value.visible = False
if return_output:
return converted_datasets
return f"The file conversion of {converter.name} on data {original_dataset.hid} has been added to the Queue."
# We need to clear associated files before we set metadata
# so that as soon as metadata starts to be set, e.g. implicitly converted datasets are deleted and no longer available 'while' metadata is being set, not just after
# We'll also clear after setting metadata, for backwards compatibility
def __new_composite_file(
self,
name: str,
optional: bool = False,
mimetype: Optional[str] = None,
description: Optional[str] = None,
substitute_name_with_metadata: Optional[str] = None,
is_binary: bool = False,
to_posix_lines: bool = True,
space_to_tab: bool = False,
**kwds,
) -> Bunch:
kwds["name"] = name
kwds["optional"] = optional
kwds["mimetype"] = mimetype
kwds["description"] = description
kwds["substitute_name_with_metadata"] = substitute_name_with_metadata
kwds["is_binary"] = is_binary
kwds["to_posix_lines"] = to_posix_lines
kwds["space_to_tab"] = space_to_tab
composite_file = Bunch(**kwds)
return composite_file
[docs]
def add_composite_file(self, name: str, **kwds) -> None:
# self.composite_files = self.composite_files.copy()
self.composite_files[name] = self.__new_composite_file(name, **kwds)
@property
def writable_files(self):
files = {}
if self.composite_type != "auto_primary_file":
files[self.primary_file_name] = self.__new_composite_file(self.primary_file_name)
for key, value in self.get_composite_files().items():
files[key] = value
return files
[docs]
def get_writable_files_for_dataset(self, dataset: Optional[HasMetadata]) -> Dict:
files = {}
if self.composite_type != "auto_primary_file":
files[self.primary_file_name] = self.__new_composite_file(self.primary_file_name)
for key, value in self.get_composite_files(dataset).items():
files[key] = value
return files
[docs]
def get_composite_files(self, dataset: Optional[HasMetadata] = None):
def substitute_composite_key(key, composite_file):
if composite_file.substitute_name_with_metadata:
if dataset:
meta_value = str(dataset.metadata.get(composite_file.substitute_name_with_metadata))
else:
meta_value = self.metadata_spec[composite_file.substitute_name_with_metadata].default
return key % meta_value
return key
files = {}
for key, value in self.composite_files.items():
files[substitute_composite_key(key, value)] = value
return files
[docs]
def generate_primary_file(self, dataset: HasExtraFilesAndMetadata) -> str:
raise Exception("generate_primary_file is not implemented for this datatype.")
@property
def has_resolution(self):
return False
[docs]
def matches_any(self, target_datatypes: List[Any]) -> bool:
"""
Check if this datatype is of any of the target_datatypes or is
a subtype thereof.
"""
datatype_classes = tuple(datatype if isclass(datatype) else datatype.__class__ for datatype in target_datatypes)
return isinstance(self, datatype_classes)
[docs]
@staticmethod
def merge(split_files: List[str], output_file: str) -> None:
"""
Merge files with copy.copyfileobj() will not hit the
max argument limitation of cat. gz and bz2 files are also working.
"""
if not split_files:
raise ValueError(f"Asked to merge zero files as {output_file}")
elif len(split_files) == 1:
shutil.copyfileobj(open(split_files[0], "rb"), open(output_file, "wb"))
else:
with open(output_file, "wb") as fdst:
for fsrc in split_files:
shutil.copyfileobj(open(fsrc, "rb"), fdst)
# ------------- Dataproviders
[docs]
def has_dataprovider(self, data_format: str) -> bool:
"""
Returns True if `data_format` is available in `dataproviders`.
"""
return data_format in self.dataproviders
[docs]
def dataprovider(self, dataset: DatasetProtocol, data_format: str, **settings):
"""
Base dataprovider factory for all datatypes that returns the proper provider
for the given `data_format` or raises a `NoProviderAvailable`.
"""
if self.has_dataprovider(data_format):
return self.dataproviders[data_format](self, dataset, **settings)
raise p_dataproviders.exceptions.NoProviderAvailable(self, data_format)
[docs]
def validate(self, dataset: DatasetProtocol, **kwd) -> DatatypeValidation:
return DatatypeValidation.unvalidated()
[docs]
@p_dataproviders.decorators.dataprovider_factory("base")
def base_dataprovider(self, dataset: DatasetProtocol, **settings) -> p_dataproviders.base.DataProvider:
dataset_source = p_dataproviders.dataset.DatasetDataProvider(dataset)
return p_dataproviders.base.DataProvider(dataset_source, **settings)
[docs]
@p_dataproviders.decorators.dataprovider_factory("chunk", p_dataproviders.chunk.ChunkDataProvider.settings)
def chunk_dataprovider(self, dataset: DatasetProtocol, **settings) -> p_dataproviders.chunk.ChunkDataProvider:
dataset_source = p_dataproviders.dataset.DatasetDataProvider(dataset)
return p_dataproviders.chunk.ChunkDataProvider(dataset_source, **settings)
[docs]
@p_dataproviders.decorators.dataprovider_factory("chunk64", p_dataproviders.chunk.Base64ChunkDataProvider.settings)
def chunk64_dataprovider(
self, dataset: DatasetProtocol, **settings
) -> p_dataproviders.chunk.Base64ChunkDataProvider:
dataset_source = p_dataproviders.dataset.DatasetDataProvider(dataset)
return p_dataproviders.chunk.Base64ChunkDataProvider(dataset_source, **settings)
def _clean_and_set_mime_type(self, trans, mime: str, headers: Headers) -> None:
if mime.lower() in XSS_VULNERABLE_MIME_TYPES:
if not getattr(trans.app.config, "serve_xss_vulnerable_mimetypes", True):
mime = DEFAULT_MIME_TYPE
headers["content-type"] = mime
[docs]
def handle_dataset_as_image(self, hda: DatasetProtocol) -> str:
raise Exception("Unimplemented Method")
def __getstate__(self) -> Dict[str, Any]:
state = self.__dict__.copy()
state.pop("display_applications", None)
return state
[docs]
@p_dataproviders.decorators.has_dataproviders
class Text(Data):
edam_format = "format_2330"
file_ext = "txt"
line_class = "line"
is_binary = False
# Add metadata elements
MetadataElement(
name="data_lines",
default=0,
desc="Number of data lines",
readonly=True,
optional=True,
visible=False,
no_value=0,
)
[docs]
def get_mime(self) -> str:
"""Returns the mime type of the datatype"""
return "text/plain"
[docs]
def set_meta(self, dataset: DatasetProtocol, *, overwrite: bool = True, **kwd) -> None:
"""
Set the number of lines of data in dataset.
"""
dataset.metadata.data_lines = self.count_data_lines(dataset)
[docs]
def estimate_file_lines(self, dataset: DatasetProtocol) -> Optional[int]:
"""
Perform a rough estimate by extrapolating number of lines from a small read.
"""
sample_size = 1048576
try:
with compression_utils.get_fileobj(dataset.get_file_name()) as dataset_fh:
dataset_read = dataset_fh.read(sample_size)
sample_lines = dataset_read.count("\n")
return int(sample_lines * (float(dataset.get_size()) / float(sample_size)))
except UnicodeDecodeError:
log.warning(f"Unable to estimate lines in file {dataset.get_file_name()}, likely not a text file.")
return None
[docs]
def count_data_lines(self, dataset: HasFileName) -> Optional[int]:
"""
Count the number of lines of data in dataset,
skipping all blank lines and comments.
"""
CHUNK_SIZE = 2**15 # 32Kb
data_lines = 0
with compression_utils.get_fileobj(dataset.get_file_name()) as in_file:
# FIXME: Potential encoding issue can prevent the ability to iterate over lines
# causing set_meta process to fail otherwise OK jobs. A better solution than
# a silent try/except is desirable.
try:
for line in iter_start_of_line(in_file, CHUNK_SIZE):
line = line.strip()
if line and not line.startswith("#"):
data_lines += 1
except UnicodeDecodeError:
log.warning(f"Unable to count lines in file {dataset.get_file_name()}, likely not a text file.")
return None
return data_lines
[docs]
def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
"""
Set the peek. This method is used by various subclasses of Text.
"""
line_count = kwd.get("line_count")
width = kwd.get("width", 256)
skipchars = kwd.get("skipchars")
line_wrap = kwd.get("line_wrap", True)
if not dataset.dataset.purged:
# The file must exist on disk for the get_file_peek() method
dataset.peek = get_file_peek(dataset.get_file_name(), width=width, skipchars=skipchars, line_wrap=line_wrap)
if line_count is None:
# See if line_count is stored in the metadata
if dataset.metadata.data_lines:
dataset.blurb = f"{util.commaify(str(dataset.metadata.data_lines))} {inflector.cond_plural(dataset.metadata.data_lines, self.line_class)}"
else:
# Number of lines is not known ( this should not happen ), and auto-detect is
# needed to set metadata
# This can happen when the file is larger than max_optional_metadata_filesize.
if int(dataset.get_size()) <= 1048576:
# Small dataset, recount all lines and reset peek afterward.
lc = self.count_data_lines(dataset)
if lc is not None:
dataset.metadata.data_lines = lc
dataset.blurb = f"{util.commaify(str(lc))} {inflector.cond_plural(lc, self.line_class)}"
else:
dataset.blurb = "Error: Cannot count lines in dataset"
else:
est_lines = self.estimate_file_lines(dataset)
if est_lines is not None:
dataset.blurb = f"~{util.shorten_with_metric_prefix(est_lines)} {inflector.cond_plural(est_lines, self.line_class)}"
else:
dataset.blurb = "Error: Cannot estimate lines in dataset"
else:
dataset.blurb = f"{util.commaify(str(line_count))} {inflector.cond_plural(line_count, self.line_class)}"
else:
dataset.peek = "file does not exist"
dataset.blurb = "file purged from disk"
[docs]
@classmethod
def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Optional[Dict]) -> None:
"""
Split the input files by line.
"""
if split_params is None:
return
if len(input_datasets) > 1:
raise Exception("Text file splitting does not support multiple files")
input_files = [ds.get_file_name() for ds in input_datasets]
lines_per_file = None
chunk_size = None
if split_params["split_mode"] == "number_of_parts":
lines_per_file = []
# Computing the length is expensive!
def _file_len(fname):
with open(fname) as f:
return sum(1 for _ in f)
length = _file_len(input_files[0])
parts = int(split_params["split_size"])
if length < parts:
parts = length
len_each, remainder = divmod(length, parts)
while length > 0:
chunk = len_each
if remainder > 0:
chunk += 1
lines_per_file.append(chunk)
remainder -= 1
length -= chunk
elif split_params["split_mode"] == "to_size":
chunk_size = int(split_params["split_size"])
else:
raise Exception(f"Unsupported split mode {split_params['split_mode']}")
f = open(input_files[0])
try:
chunk_idx = 0
file_done = False
part_file = None
while not file_done:
if lines_per_file is None:
this_chunk_size = chunk_size
elif chunk_idx < len(lines_per_file):
this_chunk_size = lines_per_file[chunk_idx]
chunk_idx += 1
lines_remaining = this_chunk_size
part_file = None
while lines_remaining > 0:
a_line = f.readline()
if a_line == "":
file_done = True
break
if part_file is None:
part_dir = subdir_generator_function()
part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
part_file = open(part_path, "w")
part_file.write(a_line)
lines_remaining -= 1
except Exception as e:
log.error("Unable to split files: %s", unicodify(e))
raise
finally:
f.close()
if part_file:
part_file.close()
# ------------- Dataproviders
[docs]
@p_dataproviders.decorators.dataprovider_factory("line", p_dataproviders.line.FilteredLineDataProvider.settings)
def line_dataprovider(self, dataset: DatasetProtocol, **settings) -> p_dataproviders.line.FilteredLineDataProvider:
"""
Returns an iterator over the dataset's lines (that have been stripped)
optionally excluding blank lines and lines that start with a comment character.
"""
dataset_source = p_dataproviders.dataset.DatasetDataProvider(dataset)
return p_dataproviders.line.FilteredLineDataProvider(dataset_source, **settings)
[docs]
@p_dataproviders.decorators.dataprovider_factory("regex-line", p_dataproviders.line.RegexLineDataProvider.settings)
def regex_line_dataprovider(
self, dataset: DatasetProtocol, **settings
) -> p_dataproviders.line.RegexLineDataProvider:
"""
Returns an iterator over the dataset's lines
optionally including/excluding lines that match one or more regex filters.
"""
dataset_source = p_dataproviders.dataset.DatasetDataProvider(dataset)
return p_dataproviders.line.RegexLineDataProvider(dataset_source, **settings)
[docs]
class Directory(Data):
"""Class representing a directory of files."""
file_ext = "directory"
def _archive_main_file(
self, archive: ZipstreamWrapper, display_name: str, data_filename: str
) -> Tuple[bool, str, str]:
"""Overwrites the method to not do anything.
No main file gets added to a directory archive.
"""
error, msg, messagetype = False, "", ""
return error, msg, messagetype
[docs]
class ZarrDirectory(Directory):
"""Class representing a zarr-format structure with general-purpose numeric content."""
edam_format = "format_3915"
file_ext = "zarr"
# This wouldn't be needed if the CompressedFile.extract function didn't
# create an extra folder under the dataset's extra_files_path.
# Maybe this can be avoided somehow?
MetadataElement(
name="store_root",
default=None,
desc="Name of the root folder where the zarr store is located",
readonly=True,
optional=False,
visible=False,
)
MetadataElement(
name="zarr_format",
default=None,
desc="Zarr format version",
readonly=True,
optional=False,
visible=False,
)
[docs]
def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
if not dataset.dataset.purged:
dataset.blurb = f"Format v{dataset.metadata.zarr_format}"
else:
dataset.peek = "file does not exist"
dataset.blurb = "file purged from disk"
[docs]
def sniff(self, filename: str) -> bool:
# TO DO: Can we access extra files path from here? Otherwise it cannot be auto-detected.
return False
[docs]
def display_data(
self,
trans,
dataset: DatasetHasHidProtocol,
preview: bool = False,
filename: Optional[str] = None,
to_ext: Optional[str] = None,
**kwd,
):
if preview:
store_root_path = os.path.join(dataset.extra_files_path, dataset.metadata.store_root)
metadata_file_path = self._find_zarr_metadata_file(store_root_path)
if metadata_file_path:
headers = kwd.get("headers", {})
headers["content-type"] = "application/json"
return self._yield_user_file_content(trans, dataset, metadata_file_path, headers), headers
return super().display_data(trans, dataset, preview, filename, to_ext, **kwd)
def _find_store_root_folder_name(self, dataset: DatasetProtocol) -> Optional[str]:
"""Returns the name of the root folder where the Zarr store is located.
The Zarr store can be directly in the extra files folder or in a subfolder.
"""
extra_files_path = dataset.extra_files_path
if self._find_zarr_metadata_file(extra_files_path):
return "" # The store is in the root of the extra files folder
items_in_path = os.listdir(extra_files_path)
sub_folder_name = items_in_path[0]
zarr_store_path = os.path.join(extra_files_path, sub_folder_name)
if (
len(items_in_path) == 1
and os.path.isdir(zarr_store_path)
and self._find_zarr_metadata_file(zarr_store_path)
):
return sub_folder_name # The store is in a subfolder of the extra files folder
return None # The directory structure does not look like Zarr format
def _load_zarr_metadata_file(self, store_root_path: str) -> Optional[Dict[str, Any]]:
"""Returns the path to the metadata file in the Zarr store."""
meta_file = self._find_zarr_metadata_file(store_root_path)
if meta_file:
with open(meta_file) as f:
return json.load(f)
return None
def _find_zarr_metadata_file(self, store_root_path: str) -> Optional[str]:
"""Returns the path to the metadata file in the Zarr store."""
meta_file = None
files_in_store = os.listdir(store_root_path)
# Depending on the Zarr version, the metadata file can be in different locations
# In v1 the metadata is in a file named "meta" https://zarr-specs.readthedocs.io/en/latest/v1/v1.0.html
# In v2 it can be in .zarray or .zgroup https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html
# In v3 the metadata is in a file named "zarr.json" https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html
for meta_filename in ["meta", ".zarray", ".zgroup", "zarr.json"]:
if meta_filename in files_in_store:
meta_file = os.path.join(store_root_path, meta_filename)
break
if meta_file and os.path.isfile(meta_file):
return meta_file
return None
def _get_format_version(self, store_root_path: str) -> Optional[str]:
"""Returns the Zarr format version from the metadata file in the Zarr store."""
metadata_file = self._load_zarr_metadata_file(store_root_path)
if metadata_file:
return metadata_file.get("zarr_format")
return None
[docs]
class GenericAsn1(Text):
"""Class for generic ASN.1 text format"""
edam_data = "data_0849"
edam_format = "format_1966"
file_ext = "asn1"
[docs]
class LineCount(Text):
"""
Dataset contains a single line with a single integer that denotes the
line count for a related dataset. Used for custom builds.
"""
[docs]
class Newick(Text):
"""New Hampshire/Newick Format"""
edam_data = "data_0872"
edam_format = "format_1910"
file_ext = "newick"
[docs]
def sniff(self, filename: str) -> bool:
"""Returning false as the newick format is too general and cannot be sniffed."""
return False
[docs]
@build_sniff_from_prefix
class Nexus(Text):
"""Nexus format as used By Paup, Mr Bayes, etc"""
edam_data = "data_0872"
edam_format = "format_1912"
file_ext = "nex"
[docs]
def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
"""All Nexus Files Simply puts a '#NEXUS' in its first line"""
return file_prefix.string_io().read(6).upper() == "#NEXUS"
# ------------- Utility methods --------------
# nice_size used to be here, but to resolve cyclical dependencies it's been
# moved to galaxy.util. It belongs there anyway since it's used outside
# datatypes.
nice_size = util.nice_size
[docs]
def get_test_fname(fname):
"""Returns test data filename"""
path = os.path.dirname(__file__)
full_path = os.path.join(path, "test", fname)
return full_path
[docs]
def get_file_peek(file_name, width=256, line_count=5, skipchars=None, line_wrap=True):
"""
Returns the first line_count lines wrapped to width.
>>> def assert_peek_is(file_name, expected, *args, **kwd):
... path = get_test_fname(file_name)
... peek = get_file_peek(path, *args, **kwd)
... assert peek == expected, "%s != %s" % (peek, expected)
>>> assert_peek_is('0_nonewline', u'0')
>>> assert_peek_is('0.txt', u'0\\n')
>>> assert_peek_is('4.bed', u'chr22\\t30128507\\t31828507\\tuc003bnx.1_cds_2_0_chr22_29227_f\\t0\\t+\\n', line_count=1)
>>> assert_peek_is('1.bed', u'chr1\\t147962192\\t147962580\\tCCDS989.1_cds_0_0_chr1_147962193_r\\t0\\t-\\nchr1\\t147984545\\t147984630\\tCCDS990.1_cds_0_0_chr1_147984546_f\\t0\\t+\\n', line_count=2)
"""
# Set size for file.readline() to a negative number to force it to
# read until either a newline or EOF. Needed for datasets with very
# long lines.
if width == "unlimited":
width = -1
if skipchars is None:
skipchars = []
lines = []
count = 0
last_line_break = False
with compression_utils.get_fileobj(file_name) as temp:
while count < line_count:
try:
line = temp.readline(width)
except UnicodeDecodeError:
return "binary file"
if line == "":
break
last_line_break = False
if line.endswith("\n"):
line = line[:-1]
last_line_break = True
elif not line_wrap:
for i in file_reader(temp, 1):
if i == "\n":
last_line_break = True
if not i or i == "\n":
break
skip_line = False
for skipchar in skipchars:
if line.startswith(skipchar):
skip_line = True
break
if not skip_line:
lines.append(line)
count += 1
return "\n".join(lines) + ("\n" if last_line_break else "")